Thanks John,

I suggest making this test framework perform this check by default
(the twill and API based frameworks) and seeing what - if anything -
breaks as a result on the Test Tool Shed.

Note that one area of fuzziness is subclasses, e.g. if the tool output
was labelled "fastqsanger", but the <test> just said "fastq", I would
say the test was broken. On the other hand, if the <test> used a
specific datatype like "fastqsanger" but the tool produced a dataset
tagged with a more generic datatype like "fastq" I think that is a
again a real failure.


On Fri, Mar 14, 2014 at 3:15 PM, John Chilton <> wrote:
> Grepping around the code I think this is the only way a ftype
> attribute on an output affects the evaluation of test data.
>                 if attributes.get( 'ftype', None ) == 'bam':
>                     local_fh, temp_name = self._bam_to_sam(
> local_name, temp_name )
>                     local_name =
> I am not sure it was ever meant as a strict test.
> I worry about breaking backward compatibility but it is easy enough to
> implement this as an actual check when using newer API driven tests. I
> have opened a pull request for this functionality here:
> Thoughts?
> -John
> On Tue, Mar 11, 2014 at 10:30 AM, Peter Cock <> 
> wrote:
>> That seems to work - thanks Björn :)
>> This seems to have exposed a bug in the <test> framework, e.g.
>>         <test>
>>             <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
>>             <param name="db_opts_selector" value="file" />
>>             <param name="subject" value="three_human_mRNA.fasta"
>> ftype="fasta" />
>>             <param name="database" value="" />
>>             <param name="evalue_cutoff" value="1e-40" />
>>             <param name="out_format" value="5" />
>>             <param name="adv_opts_selector" value="basic" />
>>             <output name="output1"
>> file="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" />
>>         </test>
>> This was saying the output should have been "blastxml",
>> but until I just fixed it the output was being tagged as
>> "tabular" (although did check
>> the content it didn't check the datatype matched).
>> Dave - do think this is a reasonable enhancement?
>> Peter

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